rs1150064

Positions:

• chr1-46682372-T-A
• chr1-46682372-T-C
• chr1-46682372-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014774.3(EFCAB14):​c.1312+928A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,976 control chromosomes in the GnomAD database, including 13,916 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.40 (13916 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: EFCAB14 NM_014774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

Genes affected

EFCAB14 (HGNC:29051): (EF-hand calcium binding domain 14) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

EFCAB14-AS1 (HGNC:44108): (EFCAB14 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB14	NM_014774.3	c.1312+928A>T		intron_variant		ENST00000371933.8	NP_055589.1
EFCAB14-AS1	NR_038827.1	n.268+108T>A		intron_variant, non_coding_transcript_variant
EFCAB14-AS1	NR_038828.1	n.185-4301T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB14	ENST00000371933.8	c.1312+928A>T		intron_variant		1	NM_014774.3	ENSP00000361001	P2
EFCAB14-AS1	ENST00000442839.5	n.185-4301T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60664 AN: 151824 Hom.: 13858 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.206 AC: 7 AN: 34 Hom.: 0 AF XY: 0.231 AC XY: 6 AN XY: 26

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.400 AC: 60785 AN: 151942 Hom.: 13916 Cov.: 32 AF XY: 0.407 AC XY: 30229 AN XY: 74230

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.413

Alfa AF: 0.335 Hom.: 1175

Bravo AF: 0.420

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.0
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1150064; hg19: chr1-47148044;